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Integrated G Proteins Signaling in Plants pp 251–277Cite as

Bioinformatics of Seven-Transmembrane Receptors in Plant Genomes

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Part of the book series: Signaling and Communication in Plants ((SIGCOMM))

Abstract

Seven-transmembrane receptors (7TMRs; also known as G protein-coupled receptors, GPCRs) constitute the largest receptor superfamily in metazoa. In striking contrast, very few numbers of 7TMRs are reported in plants. Comparative analysis revealed that many of 7TMR proteins found in plants are in fact unique to the plant kingdom. More interestingly, some 7TMR proteins appear to have acquired GPCR functions independently during their evolution. Furthermore, the origin(s) of 7TMR proteins goes back to the level of eukaryote–prokaryote divergence. In order to understand such deep divergence, powerful and sensitive bioinformatics tools are necessary. In this chapter, we first overview the plant 7TMR proteins and how they are distinct from metazoan counterparts. We review various computational methods that are used for classifying 7TMR proteins and their strengths and weaknesses when they are applied for this divergent protein family. We describe our recent efforts to provide a computational tool that facilitates identifying 7TMR candidates from diverse genomes.

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Notes

  1. 1.

    The original GPCRDB was updated until June 2006. Although the new GPCRDB resumed the development and updating later, as of this writing, the new GPCRDB still has only a part of the original content. Therefore, all statistics from GPCRDB in this chapter were obtained from the original GPCRDB (available from http://www.gpcr.org/7tm_old/). The new GPCRDB is available from http://www.gpcr.org/7tm/.

  2. 2.

    All % similarities are based on blastp search results. These values are obtained using only the highly similar regions aligned with blastp. The % similarity would be lower if the entire protein regions are aligned.

  3. 3.

    An E-value or expect value for similarity search is the number of hits you can expect to see by chance when searching the database. The E-value is related to the P-value (the probability), but not the same. An E-value of 1 means that you can expect to see one hit with the same score or higher simply by chance by searching the same size of a database. Similar to the P-value, lower the E-values, especially closer they are to 0, the more significant the matches are. You cannot obtain such hits purely by chance.

  4. 4.

    See other chapters of this book for more details on plant G proteins.

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Acknowledgments

The authors thank Dr. Alan Jones (University of North Carolina) for discussion and unpublished information. This work was in part funded by the grant number R01LM009219 from the National Library of Medicine to E.N.M.

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Authors and Affiliations

  1. School of Biological Sciences and Center for Plant Science Innovation, University of Nebraska-Lincoln, 403 Manter Hall, Lincoln, NE, 68588-0118, USA

    Etsuko N. Moriyama & Stephen O. Opiyo

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  1. Etsuko N. Moriyama
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  2. Stephen O. Opiyo
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Correspondence to Etsuko N. Moriyama .

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Editors and Affiliations

  1. Dept. Plant Sciences, Tel Aviv University, Ramat Aviv, Tel Aviv, 69978, Israel

    Shaul Yalovsky

  2. Inst. Zelluläre und Molekulare, Universität Bonn, Kirschallee 1, Bonn, 53115, Germany

    František Baluška

  3. Dept. Biology & Pharmacology, University of North Carolina, Coker Hall 317, Chapel Hill, 27599, U.S.A.

    Alan Jones

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Moriyama, E.N., Opiyo, S.O. (2010). Bioinformatics of Seven-Transmembrane Receptors in Plant Genomes. In: Yalovsky, S., Baluška, F., Jones, A. (eds) Integrated G Proteins Signaling in Plants. Signaling and Communication in Plants. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-03524-1_13

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